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On May 9, 1969, cars 4554-4555 entered service on the N service as part of a mixed consist with R40Ms. Although, there were some slight cosmetic differences, the R40Ms and R42s were for all practical purposes the same car type. As of January 5, 1970, all cars from 4550 to 4949 were in service.[2]

The R42s were the first cars to use solid state converters in place of the motor-generators as standard equipment.

In 1977, pantograph gates, salvaged from retired Arnines, were modified and then installed on these cars, and also on the R40Ms as a safety measure.

Between 1988 and 1989, R42s underwent overhaul as a result of deferred maintenance in the New York City Subway during the 1970s and the 1980s. 282 cars (4550–4839) were overhauled by Morrisen-Knudsen while the last 110 cars (4840–4949) were rebuilt in-house by the Coney Island Overhaul Shop in Brooklyn. The one minor difference in appearance between the two overhauls was that many cars of the Coney Island version featured the original blue door indicator lights at the ends of the cars, whereas these lights were removed from the Morrison-Knudsen rebuilds. Also, all cars became General Electric (GE) cars after rebuilding.

Cars 4680-4681, 4714-4715, and 4766-4767 were scrapped in 1988 due to various accidents. On June 6, 1995, cars 4664-4665 were involved in a collision on the Williamsburg Bridge. Car 4664 was scrapped in 2000 (with cars 4685 and 4726, which were not involved in the accident), while 4665 was mated with straight-ended R40A car #4460, which lost its mate in the same accident. On November 6, 2007, an M train of R42s was involved in an accident when the motorman attempted to relay it south of the Chambers Street station. As the R42 fleet was being retired at the time, the entire consist[3] was hauled to 207th Street Yard for reefing instead of being repaired even though only the first two cars suffered major damage.[4][5]

The R160s replaced many of the R42s in the late 2000s. They were intended to replace the entire fleet, but this has been halted due to structural issues found on the R44s. 50 cars (#4788-4817 and #4820-4839) still remain in service and are assigned to East New York Yard, operating on the J and Z trains. After retirement, most cars were stripped and sunk as artificial reefs along the Atlantic coast.